A no-deal Brexit could mean cancelled NHS operations, delays in diagnoses and long-term pressure on staffing numbers, private letters and briefing notes seen by the Guardian reveal.

The set of 30 documents released under freedom of information requests provide a detailed portrait of contingency planning for Brexit in NHS Scotland and Wales.

They say it could take years to train enough staff to replace departing EU nationals, increasing the burden on the health service at a time when staff shortages are already starting to bite. They also suggest the consequences for patients could be serious if vital medical supplies are held up.

﻿The warning of staffing shortages comes from a Welsh government “high-level summary for the country’s health and social care services after Brexit.

It says Brexit is having an impact already on the recruitment and retention of EU nationals and that the issue is most likely to affect less skilled staff.

It also says that failure to reach a deal could have a serious impact on EU staff whose professional qualifications may no longer be recognised, causing a “financial burden and delay for them to work in the UK”.

Theresa May has previously said she wants UK professional qualifications to continue to be recognised across the EU in the future, and vice-versa.

Other documents released at the request of the anti-Brexit campaign Best for Britain, include a letter from the Scottish government to health chief executives that chides them for being underprepared for Brexit and not adequately assisting staff who are EU nationals.

The letter, sent in June, says there had been a lack of preparation for Brexit. Scottish health boards had been told a year before to be pro-active in communicating with staff but there was little evidence of that happening, it says.

“It is therefore disappointing that, in our recent series of meetings, we have heard little about activity underway across boards to communicate with and support staff,” the letter says. “Given that EU withdrawal is drawing closer ... communication with staff is now ever more urgent.”

The letter also said health boards should be planning for potential impacts on the medicines and medical equipment supply chains.

Another document reveals that the Scottish government has been told to expect potential delays to operations, should the UK crash out of the EU without a deal.

A briefing note to the former Scottish health secretary Shona Robison said failure to agree a withdrawal agreement would “remove the guarantee of consistent and timely access to radioisotopes, potentially resulting in delays in diagnosis and cancelled operations for patients”.

The Scottish government said it had been reassured that NHS boards had recently improved their communications with EU nationals on their staff, and ministers told all EU employees in September their contributions were valued. Even so, the extent to which the damage and risks of Brexit could be catered for were limited, given how complex and uncertain the process was.

“We are doing everything we can to work cooperatively with the UK government on these issues,” a Scottish government spokesman said. “But this is proving very difficult indeed given how ill-prepared the UK government appears to be and how problematic it is to obtain clear information from them.”

Dr Lewis Morrison, the chair of BMA Scotland, said the biggest challenge for the NHS was knowing what a Brexit deal would protect and how it would work, though Brexit would be bad for the NHS regardless.

“A lot of the concerns exist whatever flavour of Brexit we get,” Morrison said. “The BMA opposed Brexit on this basis. There is no such thing as a Brexit which is safe for the NHS. Doctors are already under pressure without other colleagues leaving.”

The Labour MP Paul Williams, a former GP and a Best for Britain supporter, said: “Anyone who loves the NHS should be worried about Brexit’s impact on it. From staffing to funding you can see the decisions been made by Brexiteers in Westminster having an impact in local hospitals and wards.”

The Scottish and Welsh health secretaries wrote a joint letter to the immigration minister, Caroline Nokes, on Saturday, urging her to allow family members to join a UK-wide pilot scheme to allow EU nationals to remain in the UK.

The failure to include family members was raised as a specific concern in one of the documents seen by the Guardian, in the minutes of a meeting where a group of EU national dentists raised it with the Scottish first minister, Nicola Sturgeon.

The pilot gives health and social care workers, and university staff, the chance to apply for settled status before the date the UK is due to leave the EU in March 2019, but family members cannot be included and will have to wait to a later date to have their status confirmed.

A Department of Health and Social Care spokesperson said: “The government is confident of reaching a deal with the EU that benefits patients and the NHS – but we are preparing for all situations and we are working closely with partners to ensure adequate stockpiles are in place for all medicines which may be affected in the event of a no-deal Brexit.

“Staff from the EU are a vital part of our NHS and social care workforce and we want to see their excellent work continue long after we leave the European Union.”